Concatenation Analyses in the Presence of Incomplete Lineage Sorting

This article has focused on what has been established theoretically for some standard methods for estimating species trees (i.e., concatenation using maximum likelihood and summary methods such as MP-EST and ASTRAL), as well as for the newer approach of weighted statistical binning, followed by a summary method. Because the term “statistical consistency” has been used in two different ways in the literature, we have summarized what is known under each meaning: the weaker sense where both parameters (sequence length per locus and number of loci) increase, and the stronger sense where only the number of loci increases but the sequence length per locus is bounded, perhaps by a constant. We have also clarified that Roch and Steel’s theorem about concatenation using maximum likelihood being statistically inconsistent is restricted to unpartitioned maximum likelihood. So, what do we know about statistical consistency (for either sense) of standard techniques for estimating species trees in the presence of ILS? Methods that have been proven to be statistically consistent in the first sense include the standard summary methods (e.g., MP-EST, ASTRAL, the population tree from BUCKy 22, etc.), methods that estimate trees directly from alignments, such as *BEAST and SVDquartets, and also weighted statistical binning, paired with standard summary methods. On the negative side, Roch and Steel’s theorem establishes that unpartitioned maximum likelihood can be sta...
Source: PLOS Currents Tree of Life - Category: Genetics & Stem Cells Authors: Source Type: research